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      Genome Assembly Workshop 2020

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Introduction and Lectures
Intro to the Workshop and Core
Schedule
Genome Assembly
Introduction to the DNA Tech Core
A Brief Overview of Genome Annotation, with a Focus on the Use of Isoseq
Support
Cheat Sheets
Software and Links
Scripts
Prerequisites
CLI - Logging in and Transferring Files
CLI - Intro to Command-Line
CLI - Advanced Command-Line (extra)
CLI - Running jobs on the Cluster and using modules
Conda
R - Getting Started
R - Intro to R
R - Prepare Data in R (extra)
R - Data in R (extra)
More Materials (extra)
Snakemake
Introduction
Challenge Answers
K-mers
K-mers tutorial
PacBio
Introduction to PacBio HiFi Data and Applications
Genome Assembly with PacBio HiFi Data
Improved Phased Assembly (IPA) Using HiFi Data
Assembling the drosophila genome with IPA and HiFi data
ONT Assembly
Introduction to ONT
Assembly using ONT - Hands-on
Bionano
Optical mapping for accurate genome assembly, comparative genomics, and haplotype segregation
Phase Genomics
Using Proximity to Fix Assembly
Genome Assessment
BUSCO
Additional QA/QC and metrics
ETC
Closing thoughts
Workshop Photos
Github page
Report Errors
Biocore website

All documentation for the workshop is best viewed from the github.io pages

Documentation

July 20, 2020 - July 23, 2020, 9 a.m. - 5:00 p.m daily. online learning

Contact - UC Davis Bioinformatics Core, training.bioinformatics@ucdavis.edu

Genome Assembly is currently in a renaissance, with new technologies coming together to complement each other, producing high-quality reference grade assemblies. This workshop will focus on project design, library and sequencing technologies, genome assembly and data type integration process, and evaluation in a practical and informative setting.

The format will be approximately half lecture and half hands-on. The hands-on portion of the workshop will involve command-line interaction with some R, therefore prior command-line and R experience is a must to fully participate. If you are not familiar with the command line but would like to attend, listen, and learn that is OK, but we will be unable to train you in how to use the command-line and R during this workshop.

Participants must supply their own laptop/desktop with a reliable connection to the internet. The labtop/desktop should have a current versions of R version 4.0, Rstudio, and an application that allows them to ssh into a server (see this page)

The registration fee is $1,000 for UC students, postdocs, staff and faculty, $1,200 for Non-UC academic or non-profit participants and $1,700 for other participants. We accept credit cards, as well as UC Davis recharge accounts, for payment.

Industry Sponsors

Pacific Biosciences Phase Genomics Bionano Genomics

FAQ

Who should attend? … Prior course participants have included faculty, post docs, grad students, staff, and industry researchers.

What are the prerequisites? … The hands-on portion of the workshop will involve command-line interaction with some R, therefore prior command-line and R experience is a must to fully participate. If you are not familiar with the command line but would like to attend, listen, and learn that is OK, but we will be unable to train you in how to use the command-line during this workshop.

What do I need to bring? … You will need to bring your own laptop to use, and an application that will allow you to ssh into a server (e.g. Bash for windows, or terminal for Apple OSX). Computational exercises will be performed on a remote server. We can help with setup early on in the workshop. If your department does not allow you to install software on the laptop you’ll be bringing, please contact us ahead of time.

Can I bring my own data? … We will provide datasets for use during the workshop, as this helps to keep the workshop moving. There may be time, however, to discuss your own datasets and how you might work with them outside of the workshop.

How much does it cost? … The registration fee is $1,000 for UC students, postdocs, staff and faculty, $1,200 for Non-UC academic or non-profit participants and $1,700 for other participants. Late registrations (less than one month prior to the start of the workshop) are subject to a 20% fee increase. We accept credit cards, as well as UC Davis recharge accounts, for payment.

How do I apply? … All registration is “first-come, first-served”. There is no application process. So, sign up as soon as possible to ensure your place in the workshop.

Where can I find more information, including your policies? … Go to our website (bioinformatics.ucdavis.edu/training/) and check out our FAQ and Policies.

Questions

If you have any questions, please don’t hesitate to contact us at training.bioinformatics@ucdavis.edu

Register

For the remote/virtual course in July.